Magnesium in PDB 8c87: Double Mutant A(L172)C/L(L246)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv

The structure of Double Mutant A(L172)C/L(L246)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv, PDB code: 8c87 was solved by A.Gabdulkhakov, G.Selikhanov, T.Fufina, L.Vasilieva, A.Atamas, D.Yukhimchuk, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	23.45 / 2.45
Space group	P 42 21 2
Cell size a, b, c (Å), α, β, γ (°)	99.725, 99.725, 239.107, 90, 90, 90
R / Rfree (%)	25.9 / 30.8

The structure of Double Mutant A(L172)C/L(L246)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv also contains other interesting chemical elements:

Iron

(Fe)

1 atom

The binding sites of Magnesium atom in the Double Mutant A(L172)C/L(L246)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv (pdb code 8c87). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Double Mutant A(L172)C/L(L246)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv, PDB code: 8c87:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Double Mutant A(L172)C/L(L246)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Double Mutant A(L172)C/L(L246)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg302 b:19.0 occ:1.00 MG L:BCL302 0.0 19.0 1.0 NE2 M:HIS182 1.9 13.5 1.0 ND L:BCL302 2.1 13.4 1.0 NB L:BCL302 2.1 10.9 1.0 NC L:BCL302 2.1 5.9 1.0 NA L:BCL302 2.2 16.6 1.0 CE1 M:HIS182 2.9 16.4 1.0 CD2 M:HIS182 2.9 14.0 1.0 C4D L:BCL302 3.0 12.9 1.0 C1B L:BCL302 3.1 9.7 1.0 C4B L:BCL302 3.1 11.8 1.0 C1C L:BCL302 3.1 11.2 1.0 C4A L:BCL302 3.1 18.0 1.0 C4C L:BCL302 3.2 8.3 1.0 C1D L:BCL302 3.2 18.0 1.0 C1A L:BCL302 3.2 19.4 1.0 CHB L:BCL302 3.4 9.2 1.0 CHC L:BCL302 3.4 8.6 1.0 CHD L:BCL302 3.5 15.5 1.0 CHA L:BCL302 3.5 16.3 1.0 ND1 M:HIS182 4.0 12.6 1.0 CG M:HIS182 4.1 11.8 1.0 C3D L:BCL302 4.3 15.0 1.0 C2B L:BCL302 4.3 8.8 1.0 C2D L:BCL302 4.3 18.9 1.0 C3B L:BCL302 4.4 11.4 1.0 C2C L:BCL302 4.4 9.2 1.0 C3A L:BCL302 4.4 8.2 1.0 C3C L:BCL302 4.5 8.2 1.0 C2A L:BCL302 4.5 13.4 1.0 CBB M:BPH403 4.6 6.2 1.0 CD2 M:LEU183 4.9 12.2 1.0 CM5 M:SPN406 4.9 10.7 1.0 CMC L:BCL302 4.9 7.8 1.0 CBD L:BCL302 5.0 16.7 1.0 CMA L:BCL302 5.0 16.5 1.0 CE2 L:PHE181 5.0 8.7 1.0

Magnesium binding site 2 out of 4 in the Double Mutant A(L172)C/L(L246)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Double Mutant A(L172)C/L(L246)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg303 b:10.6 occ:1.00 MG L:BCL303 0.0 10.6 1.0 NE2 L:HIS173 1.9 9.9 1.0 ND L:BCL303 2.0 21.9 1.0 NB L:BCL303 2.1 11.1 1.0 NC L:BCL303 2.2 11.5 1.0 NA L:BCL303 2.2 9.6 1.0 CE1 L:HIS173 2.6 10.3 1.0 C4D L:BCL303 3.0 20.4 1.0 C1B L:BCL303 3.1 13.6 1.0 C4B L:BCL303 3.1 12.2 1.0 CD2 L:HIS173 3.1 14.2 1.0 C1D L:BCL303 3.2 20.7 1.0 C1C L:BCL303 3.2 16.4 1.0 C4A L:BCL303 3.2 7.7 1.0 C4C L:BCL303 3.2 22.8 1.0 C1A L:BCL303 3.3 8.9 1.0 CHB L:BCL303 3.4 8.4 1.0 CHC L:BCL303 3.4 14.7 1.0 CHA L:BCL303 3.5 22.1 1.0 CHD L:BCL303 3.5 18.0 1.0 CBB M:BCL402 3.7 7.5 1.0 CAB M:BCL402 3.8 11.6 1.0 ND1 L:HIS173 3.9 7.8 1.0 OBB M:BCL402 3.9 14.2 1.0 CG L:HIS173 4.1 14.9 1.0 C3D L:BCL303 4.2 19.0 1.0 C2B L:BCL303 4.3 17.0 1.0 C2D L:BCL303 4.3 19.9 1.0 C3B L:BCL303 4.3 12.4 1.0 C3A L:BCL303 4.4 10.6 1.0 C2C L:BCL303 4.5 12.0 1.0 C3C L:BCL303 4.5 13.0 1.0 C2A L:BCL303 4.5 7.4 1.0 C3B M:BCL402 4.6 15.5 1.0 CMA L:BCL303 4.7 12.8 1.0 CD2 L:PHE167 4.7 14.5 1.0 CBD L:BCL303 5.0 13.6 1.0

Magnesium binding site 3 out of 4 in the Double Mutant A(L172)C/L(L246)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Double Mutant A(L172)C/L(L246)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv within 5.0Å range: probe atom residue distance (Å) B Occ L:Mg304 b:14.2 occ:1.00 MG L:BCL304 0.0 14.2 1.0 NE2 L:HIS153 1.9 21.2 1.0 ND L:BCL304 2.0 13.4 1.0 NB L:BCL304 2.1 6.7 1.0 NC L:BCL304 2.1 7.5 1.0 NA L:BCL304 2.2 8.5 1.0 CD2 L:HIS153 2.9 15.8 1.0 CE1 L:HIS153 2.9 15.0 1.0 C4D L:BCL304 3.0 12.8 1.0 C4B L:BCL304 3.1 6.7 1.0 C1B L:BCL304 3.1 8.5 1.0 C1C L:BCL304 3.1 8.7 1.0 C4A L:BCL304 3.1 12.5 1.0 C1D L:BCL304 3.1 13.6 1.0 C4C L:BCL304 3.2 7.9 1.0 C1A L:BCL304 3.2 9.7 1.0 CHC L:BCL304 3.4 10.4 1.0 CHB L:BCL304 3.4 8.6 1.0 CHA L:BCL304 3.5 6.6 1.0 CHD L:BCL304 3.5 9.5 1.0 ND1 L:HIS153 4.0 16.7 1.0 CG L:HIS153 4.0 12.6 1.0 C3D L:BCL304 4.2 19.6 1.0 C2D L:BCL304 4.3 14.6 1.0 C2B L:BCL304 4.3 7.4 1.0 C3B L:BCL304 4.3 9.7 1.0 C3A L:BCL304 4.4 7.0 1.0 C2C L:BCL304 4.4 8.1 1.0 C3C L:BCL304 4.5 5.6 1.0 C2A L:BCL304 4.5 8.8 1.0 CBB L:BPH305 4.5 5.9 1.0 CD1 L:LEU154 4.5 12.8 1.0 CMA L:BCL304 4.7 10.4 1.0 CE2 M:TYR210 4.8 11.1 1.0 CBD L:BCL304 4.9 13.0 1.0 CBC L:BCL304 5.0 8.1 1.0

Magnesium binding site 4 out of 4 in the Double Mutant A(L172)C/L(L246)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Double Mutant A(L172)C/L(L246)C Structure of Photosynthetic Reaction Center From Cereibacter Sphaeroides Strain Rv within 5.0Å range: probe atom residue distance (Å) B Occ M:Mg402 b:14.7 occ:1.00 MG M:BCL402 0.0 14.7 1.0 NE2 M:HIS202 1.9 11.0 1.0 ND M:BCL402 2.1 15.3 1.0 NB M:BCL402 2.1 15.4 1.0 NC M:BCL402 2.1 19.7 1.0 NA M:BCL402 2.2 15.4 1.0 CE1 M:HIS202 2.8 10.8 1.0 C4D M:BCL402 3.0 15.2 1.0 CD2 M:HIS202 3.0 16.3 1.0 C1C M:BCL402 3.1 14.3 1.0 C1B M:BCL402 3.1 12.2 1.0 C4B M:BCL402 3.1 13.7 1.0 C4C M:BCL402 3.2 14.3 1.0 C4A M:BCL402 3.2 14.7 1.0 C1D M:BCL402 3.2 18.6 1.0 C1A M:BCL402 3.3 9.6 1.0 CHC M:BCL402 3.4 9.8 1.0 CHB M:BCL402 3.4 15.8 1.0 CHA M:BCL402 3.5 11.6 1.0 CBB L:BCL303 3.5 11.5 1.0 CHD M:BCL402 3.5 13.6 1.0 ND1 M:HIS202 3.9 11.8 1.0 CAB L:BCL303 4.0 23.9 1.0 CG M:HIS202 4.1 15.9 1.0 C3D M:BCL402 4.3 11.9 1.0 C2B M:BCL402 4.3 12.6 1.0 C2D M:BCL402 4.4 19.9 1.0 OBB L:BCL303 4.4 16.4 1.0 C3B M:BCL402 4.4 15.5 1.0 C2C M:BCL402 4.4 10.8 1.0 C3C M:BCL402 4.5 12.7 1.0 C3A M:BCL402 4.5 13.7 1.0 C2A M:BCL402 4.5 5.8 1.0 CD1 M:LEU196 4.7 7.9 1.0 C3B L:BCL303 4.7 12.4 1.0 CBD M:BCL402 4.9 12.6 1.0

G.Selikhanov, A.Atamas, D.Yukhimchuk, T.Fufina, L.Vasilieva, A.Gabdulkhakov. Stabilization of Cereibacter Sphaeroides Photosynthetic Reaction Center By the Introduction of Disulfide Bonds. Membranes (Basel) V. 13 2023.
ISSN: ESSN 2077-0375
PubMed: 36837657
DOI: 10.3390/MEMBRANES13020154